Residents loaded their mattresses, cooking pots and furniture onto pickup trucks and wheelbarrows or simply carried them out of the slum on their backs.
Many headed to the nearby Eastleigh neighbourhood and found shelter in churches or a sports centre.
"I have never witnessed in my life anything like what is happening," Jane Wachira, a 37-year-old mother of three, told The Associated Press news agency as she left the slum. "My children and I are traumatised."
Police have denied using excessive force, saying they are doing what is necessary to wipe out the sect, which is accused of causing the deaths of at least 20 people in the past three months, including 12 found mutilated or beheaded since May.
|Slum residents have accused the police |
of indiscriminate violence [EPA]
The government has warned that the crackdown will continue.
Mungiki claims to have thousands of adherents drawn from the Kikuyu, Kenya's largest tribe.
Members of the group, whose name means "multitude" in the Kikuyu language, claim to be inspired by the 1950s Mau Mau uprising against British rule.
But they have become linked to murder, political violence and extortion.
Ken Ouko, a lecturer in sociology at the University of Nairobi, said the crackdown was doomed to fail because the group is an underground gang.
He said: "The problem lies in the fact that the government doesn't know whom they are wiping out.
"You cannot crack down someone you can't see. The sect members are slippery and they do their work with secrecy."
The recent bloodshed has raised fears that Mungiki members are out to disrupt elections in December, when Mwai Kibaki, the Kenyan presdient, will seek a second term.